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We acquired a new company and merged them into our existing company. We contacted suppliers prior to the change to advise that the company we acquired would no longer exist from a set date so they should invoice us going forward. A couple of suppliers are still sending invoices in the old company name which now does not exist and are making it difficult to allow the change.

Even though the invoice is made out to the old company can we still process these if absolutely necessary whilst we wait for them to update their systems?

I would pay them assuming both companies are in the same vat group with a note to suppliers to change the details (rather than not settling the invoice). In most cases this is simply the case of administration gaps where our communication didn't reach the right people to do the required changes.

Your assumption is flawed though, there is no "both" companies, the one to whom the problem invoices are addressed does not exist.

Send the invoices back, tell them you can't pay them, it creates a number of potential issues for you and the invoices shouldn't have been issued in the first place without the change you gave them plenty of notice for being implemented.

I appreciate the best option would be not to pay the invoice until they change the name but some of these are utility suppliers so we need to pay them to keep the lights on. Also some payments were already taken by DD.

It's a common enough occurrence - companies change names. Changes of ownership, reorganisation, insolvency can all result in a change of legal entity while the underlying business continues.

Completely agree that you should ensure that suppliers update their invoicing details. But there is rarely any doubt that 'you' are the customer and have ordered and received the goods or services in question.